CCM2 c.803+89C>A
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 25.4%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +89 | deep intronic (+89 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.24 | GERP -2, phastCons 0.001 |
| Overall | ||
| CADD | 0.203 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
25.4%
African / African-American · 16,484/64,852 alleles
Filtering AF
25.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 25%
Overall
3.94%
42,657/1,081,780 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 25.4% | 4 |
| South Asian | 6.85% | 15 |
| Amishnot grpmax-eligible | 6.47% | 15 |
| Middle Eastern | 4.93% | 20 |
| Ashkenazi Jewishnot grpmax-eligible | 4.74% | 21 |
| Remaining individualsnot grpmax-eligible | 4.16% | 24 |
| Admixed American | 2.6% | 39 |
| European (non-Finnish) | 2.17% | 46 |
| Finnishnot grpmax-eligible | 0.868% | 115 |
| East Asian | 0.106% | 942 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CCM2
- Coding
- c.803+89C>A
- MANE Select
- NM_031443
- dbSNP
- rs11977608
- Type
- single nucleotide variant
- Location
- chr7:45072872 (GRCh38)
- Gene constraint
- LOEUF 0.753 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.48 · 8 PDB
Similar variants
- CCM2 c.289-1G>A Pathogenic/Likely pathogenic ★★ same type
- CCM2 c.30+1G>A Pathogenic ★★ same type
- CCM2 c.472+1G>C Pathogenic/Likely pathogenic ★★ same type
- CCM2 c.473-1G>T Pathogenic ★★ same type
- CCM2 c.745+1G>T Pathogenic ★★ same type
- CCM2 p.Arg19Ter Pathogenic ★★ same type
- CCM2 p.Arg57Ter Pathogenic/Likely pathogenic ★★ same type
- CCM2 p.Gln107Ter Pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ccm2-c-803-plus-89c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown